Integrated omics and functional validation identify StGDPD1 as a central regulator of salt stress tolerance in potato.

Soil salinization poses a major threat to global agricultural productivity, particularly for salt-sensitive crops such as potato (Solanum tuberosum L.). However, the genetic and metabolic mechanisms underlying salt tolerance in potato remain poorly understood. Here, we conducted hydroponic screening of ten potato varieties under NaCl stress and identified Dongnong 303 (DN303) as a highly salt-tolerant genotype. Physiological analyses revealed that DN303 maintained root growth and exhibited enhanced antioxidant activity and osmoprotectant accumulation under salt stress. Integrated transcriptomic and metabolomic profiling revealed that glycerophospholipid metabolism, carbohydrate metabolism, and redox regulation were central to DN303's stress response. Notably, the StGDPD1 gene, encoding a glycerophosphodiester phosphodiesterase, was strongly upregulated under salt stress and associated with increased levels of glycerol-3-phosphate (G3P), a metabolite involved in membrane lipid remodeling and osmotic regulation. Functional validation showed that StGDPD1 overexpression enhanced salt tolerance, while CRISPR-Cas9 knockout lines were hypersensitive to salt stress, with reduced G3P content and impaired antioxidant defense. These findings establish StGDPD1 as a key positive regulator of salt tolerance in potato and highlight the importance of lipid metabolic pathways in abiotic stress adaptation. This work provides a mechanistic foundation and candidate gene for breeding salt-tolerant potato varieties.